Uses of Interface
sc.fiji.snt.annotation.BrainAnnotation

Packages that use BrainAnnotation

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.analysis.graph	Classes for handling neuronal reconstructions as graphs
sc.fiji.snt.annotation	Classes handling neuropil annotations and atlases metadata.
sc.fiji.snt.seed
sc.fiji.snt.util	Miscellaneous SNT utilities, including classes defining reconstruction nodes.
sc.fiji.snt.viewer	Visualization of reconstructions
sc.fiji.snt.viewer.geditor	Classes implementing SNT's Graph Viewer

Uses of BrainAnnotation in sc.fiji.snt

Methods in sc.fiji.snt that return BrainAnnotation

Modifier and Type	Method	Description
BrainAnnotation	Path.getNodeAnnotation(int pos)	Returns the neuropil annotation associated with this node.

Methods in sc.fiji.snt with parameters of type BrainAnnotation

Modifier and Type	Method	Description
void	Path.setNodeAnnotation(BrainAnnotation annotation, int pos)	Assigns an annotation to an existing node.

Uses of BrainAnnotation in sc.fiji.snt.analysis

Methods in sc.fiji.snt.analysis that return types with arguments of type BrainAnnotation

Modifier and Type	Method	Description
Map<BrainAnnotation,Integer>	NodeStatistics.getAnnotatedFrequencies()	Retrieves the count frequencies across brain compartment.
Map<BrainAnnotation,Integer>	NodeStatistics.getAnnotatedFrequencies(int level)	Retrieves the count frequencies across brain compartment.
Map<BrainAnnotation,Integer>	NodeStatistics.getAnnotatedFrequencies(int level, String hemisphere)	Retrieves the count frequencies across brain compartment.
Map<BrainAnnotation,int[]>	NodeStatistics.getAnnotatedFrequenciesByHemisphere(int level, Tree tree)
Map<BrainAnnotation,Double>	MultiTreeStatistics.getAnnotatedLength(int level)
Map<BrainAnnotation,Double>	MultiTreeStatistics.getAnnotatedLength(int level, String hemisphere)
Map<BrainAnnotation,Double>	MultiTreeStatistics.getAnnotatedLength(int level, String hemisphere, boolean norm)
Map<BrainAnnotation,Double>	TreeStatistics.getAnnotatedLength(int level)	Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
Map<BrainAnnotation,Double>	TreeStatistics.getAnnotatedLength(int level, String hemisphere)	Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
Map<BrainAnnotation,Double>	TreeStatistics.getAnnotatedLength(int level, String hemisphere, boolean norm)	Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron.
protected static Map<BrainAnnotation,Double>	TreeStatistics.getAnnotatedLength(DirectedWeightedGraph graph, int level, char lr, boolean norm)
Map<BrainAnnotation,double[]>	MultiTreeStatistics.getAnnotatedLengthsByHemisphere(int level)
Map<BrainAnnotation,double[]>	TreeStatistics.getAnnotatedLengthsByHemisphere(int level)	Retrieves the amount of cable length present on each brain compartment innervated by the analyzed neuron in the two brain hemispheres.
protected static Map<BrainAnnotation,double[]>	TreeStatistics.getAnnotatedLengthsByHemisphere(DirectedWeightedGraph graph, int level, boolean norm)
Map<BrainAnnotation,Set<T>>	NodeStatistics.getAnnotatedNodes()	Splits the nodes being analyzed into groups sharing the same brain annotation.
Map<BrainAnnotation,Set<T>>	NodeStatistics.getAnnotatedNodes(int level)	Splits the nodes being analyzed into groups sharing the same brain annotation.
Set<BrainAnnotation>	MultiTreeStatistics.getAnnotations()
Set<BrainAnnotation>	MultiTreeStatistics.getAnnotations(int level)
Set<BrainAnnotation>	TreeStatistics.getAnnotations()	Retrieves the brain compartments (neuropil labels) associated with the Tree being measured innervated by the analyzed neuron.
Set<BrainAnnotation>	TreeStatistics.getAnnotations(int depth)	Retrieves the brain compartments (neuropil labels) associated with the Tree being measured innervated by the analyzed neuron.

Methods in sc.fiji.snt.analysis with parameters of type BrainAnnotation

Modifier and Type	Method	Description
protected boolean	TreeStatistics.contains(BrainAnnotation annot, BrainAnnotation annotToBeTested, boolean includeChildren)
List<T>	NodeStatistics.get(BrainAnnotation compartment)	Gets the list of nodes associated with the specified compartment (neuropil label).
List<T>	NodeStatistics.get(BrainAnnotation compartment, boolean includeChildren)	Gets the list of nodes associated with the specified compartment (neuropil label).
Set<PointInImage>	TreeStatistics.getBranchPoints(BrainAnnotation annot)	Gets the position of all the branch points in the analyzed tree associated with the specified annotation.
Set<PointInImage>	TreeStatistics.getBranchPoints(BrainAnnotation annot, boolean includeChildren)	Gets the position of all the branch points in the analyzed tree associated with the specified annotation.
double	MultiTreeStatistics.getCableLength(BrainAnnotation compartment)
double	TreeStatistics.getCableLength(BrainAnnotation compartment)	Gets the cable length associated with the specified compartment (neuropil label).
double	TreeStatistics.getCableLength(BrainAnnotation compartment, boolean includeChildren)	Gets the cable length associated with the specified compartment (neuropil label).
double	TreeStatistics.getCableLengthNorm(BrainAnnotation compartment)	Gets the cable length associated with the specified compartment (neuropil label) as a ratio of total length.
double	TreeStatistics.getCableLengthNorm(BrainAnnotation compartment, boolean includeChildren)	Gets the cable length associated with the specified compartment (neuropil label) as a ratio of total length.
int	TreeStatistics.getNBranchPoints(BrainAnnotation annot)	Gets the number of branch points in the analyzed tree associated with the specified annotation.
int	TreeStatistics.getNBranchPoints(BrainAnnotation annot, boolean includeChildren)	Gets the number of branch points in the analyzed tree associated with the specified annotation.
double	TreeStatistics.getNBranchPointsNorm(BrainAnnotation annot)	Gets the percentage of branch points in the analyzed tree associated with the specified annotation
double	TreeStatistics.getNBranchPointsNorm(BrainAnnotation annot, boolean includeChildren)	Gets the percentage of branch points in the analyzed tree associated with the specified annotation
int	TreeStatistics.getNTips(BrainAnnotation annot)	Gets the number of end points in the analyzed tree associated with the specified annotation.
int	TreeStatistics.getNTips(BrainAnnotation annot, boolean includeChildren)	Gets the number of end points in the analyzed tree associated with the specified annotation.
double	TreeStatistics.getNTipsNorm(BrainAnnotation annot)	Gets the number of end points in the analyzed tree associated with the specified annotation.
double	TreeStatistics.getNTipsNorm(BrainAnnotation annot, boolean includeChildren)	Gets the percentage of end points in the analyzed tree associated with the specified annotation
Set<PointInImage>	TreeStatistics.getTips(BrainAnnotation annot)	Gets the position of all the tips in the analyzed tree associated with the specified annotation.
Set<PointInImage>	TreeStatistics.getTips(BrainAnnotation annot, boolean includeChildren)	Gets the position of all the tips in the analyzed tree associated with the specified annotation.

Method parameters in sc.fiji.snt.analysis with type arguments of type BrainAnnotation

Modifier and Type	Method	Description
protected SNTChart	TreeStatistics.getAnnotatedLengthHistogram(Map<BrainAnnotation,Double> map, int depth, String secondaryLabel)
SNTChart	GroupedTreeStatistics.getBoxPlot(String feature, Collection<BrainAnnotation> annotations)	Assembles a Box and Whisker Plot for the specified feature (absolute measurements).
SNTChart	GroupedTreeStatistics.getBoxPlot(String feature, Collection<BrainAnnotation> annotations, double cutoff, boolean normalize)	Assembles a Box and Whisker Plot for the specified feature.
SNTChart	GroupedTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.
SNTChart	GroupedTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature.
SNTChart	MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations)
SNTChart	MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, boolean normalize)
SNTChart	MultiTreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize)
SNTChart	TreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.
SNTChart	TreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature using "mean" as integration statistic, and no cutoff value.
SNTChart	TreeStatistics.getFlowPlot(String feature, Collection<BrainAnnotation> annotations, String statistic, double cutoff, boolean normalize)	Assembles a Flow plot (aka Sankey diagram) for the specified feature.

Uses of BrainAnnotation in sc.fiji.snt.analysis.graph

Methods in sc.fiji.snt.analysis.graph that return BrainAnnotation

Modifier and Type	Method	Description
BrainAnnotation	AnnotationWeightedEdge.getSource()
BrainAnnotation	AnnotationWeightedEdge.getTarget()

Methods in sc.fiji.snt.analysis.graph that return types with arguments of type BrainAnnotation

Modifier and Type	Method	Description
Set<BrainAnnotation>	AnnotationGraph.removeOrphans()

Uses of BrainAnnotation in sc.fiji.snt.annotation

Classes in sc.fiji.snt.annotation that implement BrainAnnotation

Modifier and Type	Class	Description
class	AllenCompartment	Defines an Allen Reference Atlas (ARA) [Allen Mouse Common Coordinate Framework] annotation.
class	DrosophilaCompartment	Represents a brain region from the Drosophila Anatomy Ontology (FBbt).
class	InsectBrainCompartment

Methods in sc.fiji.snt.annotation that return BrainAnnotation

Modifier and Type	Method	Description
BrainAnnotation	BrainAnnotation.getAncestor(int level)	Returns the ancestor of this compartment at the specified level.
BrainAnnotation	DrosophilaCompartment.getAncestor(int level)
BrainAnnotation	InsectBrainCompartment.getAncestor(int level)
BrainAnnotation	BrainAnnotation.getParent()	Returns the parent of this compartment.
BrainAnnotation	DrosophilaCompartment.getParent()
BrainAnnotation	InsectBrainCompartment.getParent()

Methods in sc.fiji.snt.annotation that return types with arguments of type BrainAnnotation

Modifier and Type	Method	Description
static Comparator<BrainAnnotation>	BrainAnnotation.comparator()

Methods in sc.fiji.snt.annotation with parameters of type BrainAnnotation

Modifier and Type	Method	Description
boolean	AllenCompartment.includes(BrainAnnotation other)
boolean	AllenCompartment.isChildOf(BrainAnnotation parentCompartment)	Assesses if this annotation is a child of a specified compartment.
boolean	BrainAnnotation.isChildOf(BrainAnnotation annotation)	Returns whether this compartment is a sub-compartment of annotation.
boolean	DrosophilaCompartment.isChildOf(BrainAnnotation annotation)
boolean	InsectBrainCompartment.isChildOf(BrainAnnotation annotation)
boolean	AllenCompartment.isParentOf(BrainAnnotation childCompartment)	Assesses if this annotation is the parent of the specified compartment.
boolean	BrainAnnotation.isParentOf(BrainAnnotation parentCompartment)	Returns whether this compartment is a parent of parentCompartment.
boolean	DrosophilaCompartment.isParentOf(BrainAnnotation annotation)
boolean	InsectBrainCompartment.isParentOf(BrainAnnotation parentCompartment)
protected void	InsectBrainCompartment.setParent(BrainAnnotation parent)
static String	BrainAnnotation.simplifiedString(BrainAnnotation annotation)

Uses of BrainAnnotation in sc.fiji.snt.seed

Methods in sc.fiji.snt.seed that return BrainAnnotation

Modifier and Type	Method	Description
BrainAnnotation	SeedPoint.getAnnotation()

Methods in sc.fiji.snt.seed with parameters of type BrainAnnotation

Modifier and Type	Method	Description
void	SeedPoint.setAnnotation(BrainAnnotation annotation)

Uses of BrainAnnotation in sc.fiji.snt.util

Methods in sc.fiji.snt.util that return BrainAnnotation

Modifier and Type	Method	Description
BrainAnnotation	PointInImage.getAnnotation()
BrainAnnotation	SNTPoint.getAnnotation()
BrainAnnotation	SWCPoint.getAnnotation()

Methods in sc.fiji.snt.util with parameters of type BrainAnnotation

Modifier and Type	Method	Description
void	PointInImage.setAnnotation(BrainAnnotation annotation)
void	SNTPoint.setAnnotation(BrainAnnotation annotation)	Assigns a neuropil annotation (e.g., atlas compartment) to this point.
void	SWCPoint.setAnnotation(BrainAnnotation annotation)

Uses of BrainAnnotation in sc.fiji.snt.viewer

Methods in sc.fiji.snt.viewer that return BrainAnnotation

Modifier and Type	Method	Description
BrainAnnotation	OBJMesh.getSourceAnnotation()	Returns the BrainAnnotation (atlas compartment) from which this mesh was retrieved, or null if this mesh was loaded from a standalone file.

Methods in sc.fiji.snt.viewer with parameters of type BrainAnnotation

Modifier and Type	Method	Description
void	OBJMesh.setSourceAnnotation(BrainAnnotation annotation)	Associates this mesh with the BrainAnnotation (atlas compartment) it was retrieved from.

Uses of BrainAnnotation in sc.fiji.snt.viewer.geditor

Methods in sc.fiji.snt.viewer.geditor with parameters of type BrainAnnotation

Modifier and Type	Method	Description
void	AnnotationGraphAdapter.setVertexColor(BrainAnnotation vertex, org.scijava.util.ColorRGB color)